Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:593128 original size:17 final size:17
Alignment explanation
Indices: 593106--593143 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
593096 GTTGAACAAG
593106 TTCTTCTCA-TTATGAAC
1 TTCTTCTCATTTA-GAAC
*
593123 TTCTTCTCCTTTAGAAC
1 TTCTTCTCATTTAGAAC
593140 TTCT
1 TTCT
593144 ATTCAAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.18, C:0.26, G:0.05, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTTAGAAC
Found at i:593740 original size:22 final size:21
Alignment explanation
Indices: 593712--593764 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
593702 TTGGCTGGGT
593712 AGTATCGATACTCTGTTCATAG
1 AGTATCGATACT-TGTTCATAG
* *
593734 AGTATCGATA-TTGTTCCTTG
1 AGTATCGATACTTGTTCATAG
*
593754 GGTATCGATAC
1 AGTATCGATAC
593765 CCAATGGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.59
21 1 0.04
22 10 0.37
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTTGTTCATAG
Found at i:594939 original size:14 final size:15
Alignment explanation
Indices: 594913--594942 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
594903 GTTTCATCTT
594913 TATTTTGAATGATGA
1 TATTTTGAATGATGA
594928 TATTTT-AATGATGA
1 TATTTTGAATGATGA
594942 T
1 T
594943 TTCGACGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TATTTTGAATGATGA
Found at i:595134 original size:10 final size:9
Alignment explanation
Indices: 595104--595205 Score: 53
Period size: 10 Copynumber: 10.2 Consensus size: 9
595094 TTATCATAAA
595104 TTTAATAGTCT
1 TTTAATA-T-T
595115 TTTGAATATT
1 TTT-AATATT
595125 TTATAATATT
1 TT-TAATATT
*
595135 ATTAAT-TT
1 TTTAATATT
**
595143 TAAAAATATCT
1 T-TTAATAT-T
595154 TTTAATATT
1 TTTAATATT
595163 TTTAAATAAATT
1 TTT-AAT--ATT
595175 TTTAAATATT
1 TTT-AATATT
595185 TTTATATATT
1 TTTA-ATATT
**
595195 AATAATATT
1 TTTAATATT
595204 TT
1 TT
595206 AAAATAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
8 2 0.03
9 17 0.24
10 32 0.44
11 7 0.10
12 14 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTAATATT
Found at i:595166 original size:22 final size:22
Alignment explanation
Indices: 595140--595188 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
595130 ATATTATTAA
595140 TTTTAAA-AATATCTTTT-AATAT
1 TTTTAAATAA-AT-TTTTAAATAT
595162 TTTTAAATAAATTTTTAAATAT
1 TTTTAAATAAATTTTTAAATAT
595184 TTTTA
1 TTTTA
595189 TATATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAATAAATTTTTAAATAT
Found at i:595205 original size:28 final size:26
Alignment explanation
Indices: 595119--595208 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 26
595109 TAGTCTTTTG
* *
595119 AATATTTTATAATATTATTAATTTTAAA
1 AATATTTTA-AATATTTTTAATATT-AA
*
595147 AATATCTTTTAATATTTTTAA-A-T-A
1 AATAT-TTTAAATATTTTTAATATTAA
595171 AAT-TTTTAAATATTTTTATATATTAA
1 AATATTTTAAATATTTTTA-ATATTAA
595197 TAATATTTTAAA
1 -AATATTTTAAA
595209 ATAATAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
22 13 0.25
23 2 0.04
24 5 0.10
25 1 0.02
26 2 0.04
27 3 0.06
28 22 0.43
29 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATTTTAAATATTTTTAATATTAA
Found at i:595220 original size:14 final size:13
Alignment explanation
Indices: 595156--595223 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 13
595146 AAATATCTTT
*
595156 TAATATTTTTAAA
1 TAATATTTTAAAA
*
595169 TAA-ATTTTTAAA
1 TAATATTTTAAAA
*
595181 T-ATTTTTATATATTAA
1 TAATATTT-TA-A--AA
595197 TAATATTTTAAAA
1 TAATATTTTAAAA
595210 TAATAATTTTAAAA
1 TAAT-ATTTTAAAA
595224 ATTCTAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 13 0.29
13 10 0.22
14 10 0.22
15 1 0.02
16 5 0.11
17 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATATTTTAAAA
Found at i:595234 original size:42 final size:41
Alignment explanation
Indices: 595156--595235 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
595146 AAATATCTTT
* * * * *
595156 TAATATTTTTAAATAAATTTTTAAATATTTTTATATATTAA
1 TAATATTTTAAAATAAAATTTTAAAAATTCTAATATATTAA
595197 TAATATTTTAAAATAATAATTTTAAAAATTCTAATATAT
1 TAATATTTTAAAATAA-AATTTTAAAAATTCTAATATAT
595236 CACGTGACGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 15 0.45
42 18 0.55
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (41 bp):
TAATATTTTAAAATAAAATTTTAAAAATTCTAATATATTAA
Found at i:598289 original size:14 final size:15
Alignment explanation
Indices: 598263--598292 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
598253 GTTTCATCTT
598263 TATTTTGAATGATGA
1 TATTTTGAATGATGA
598278 TATTTT-AATGATGA
1 TATTTTGAATGATGA
598292 T
1 T
598293 TTCGATGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TATTTTGAATGATGA
Found at i:598552 original size:20 final size:19
Alignment explanation
Indices: 598514--598564 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
598504 CTTTTTATAC
598514 TTTAAATAAATTTAAAATATT
1 TTTAAAT-AA-TTAAAATATT
598535 TTTAAATAATTAATAATATT
1 TTTAAATAATTAA-AATATT
*
598555 TTAAAATAAT
1 TTTAAATAAT
598565 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 17 0.61
21 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAATAATTAAAATATT
Found at i:598564 original size:13 final size:14
Alignment explanation
Indices: 598546--598574 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
598536 TTAAATAATT
598546 AATAAT-ATTTTAA
1 AATAATAATTTTAA
598559 AATAATAATTTTAA
1 AATAATAATTTTAA
598573 AA
1 AA
598575 ATTCTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAATAATTTTAA
Found at i:598566 original size:16 final size:15
Alignment explanation
Indices: 598529--598576 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
598519 ATAAATTTAA
*
598529 AATATTTTTAAATAATT
1 AATAATTTTAAA-AA-T
*
598546 AATAATATTTTAAAAT
1 AATAAT-TTTAAAAAT
598562 AATAATTTTAAAAAT
1 AATAATTTTAAAAAT
598577 TCTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 7 0.26
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAATTTTAAAAAT
Found at i:599859 original size:37 final size:35
Alignment explanation
Indices: 599749--600185 Score: 285
Period size: 38 Copynumber: 11.9 Consensus size: 35
599739 GTCCGGGGTT
* * * *
599749 TATATAATATATAGTTGTTAGAAGATGGTTTTTGAAAA
1 TATATATTATATAGTT-TT-GAAAAT-ATTTTTAAAAA
* * * *
599787 CATATAATATAT-GCTTT-AAAATCGATTTTTGAAAA
1 TATATATTATATAGTTTTGAAAAT--ATTTTTAAAAA
**
599822 TATATATTATATAGTTTTGAAAACGGTTTTCTAAAAATA
1 TATATATTATATAGTTTTGAAAA-TATTTT-T-AAAA-A
*
599861 TATATATTATATAGTTTTGAAAAT-TTTTGAAAATA
1 TATATATTATATAGTTTTGAAAATATTTTTAAAA-A
* *
599896 TATTTATATTATATAGTTTTTGAAAATATTTTTGAATA
1 TA--TATATTATATAG-TTTTGAAAATATTTTTAAAAA
* *
599934 TATATA-TATATAGTTTT-AAAACATTTTGAAAATA
1 TATATATTATATAGTTTTGAAAATATTTTTAAAA-A
* * *
599968 TATATATAATCTATAGTTTTTTAAAATATTTTGAAAATA
1 TATATAT--TATATAG-TTTTGAAAATATTTTTAAAA-A
* * *
600007 TATATAATATATATTTTTGAAAATGTTTTTAAAAAA
1 TATATATTATATAGTTTTGAAAATATTTTT-AAAAA
* * *
600043 TGTATATAATATATAGTTTTG-AATTTTTTTTGAAAAA
1 --TATATATTATATAGTTTTGAAAATATTTTT-AAAAA
* *
600080 TATATATTATATAGTTTTAAAAAAATAATTTTTGAAAA
1 TATATATTATATAGTTTT--GAAAAT-ATTTTTAAAAA
* *
600118 TATATTATTATAT-GTTTTGAAAACAATTTTCAAAAA
1 TATA-TATTATATAGTTTTGAAAA-TATTTTTAAAAA
** * *
600154 CGTATATAATATAGTTTTAAAAATTATTTTTA
1 TATATATTATATAGTTTTGAAAA-TATTTTTA
600186 TTTTTATTAT
Statistics
Matches: 325, Mismatches: 47, Indels: 56
0.76 0.11 0.13
Matches are distributed among these distances:
33 11 0.03
34 15 0.05
35 60 0.18
36 58 0.18
37 51 0.16
38 65 0.20
39 65 0.20
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (35 bp):
TATATATTATATAGTTTTGAAAATATTTTTAAAAA
Found at i:600007 original size:73 final size:74
Alignment explanation
Indices: 599821--600178 Score: 296
Period size: 74 Copynumber: 4.9 Consensus size: 74
599811 ATTTTTGAAA
* *
599821 ATATATATTATATAG-TTTTGAAAACGGT-TTTCTAAAAATATATATATTATATAGTTTTGAAAA
1 ATATATAATATATAGTTTTTGAAAA---TATTT-TGAAAATATATATATTATATAGTTTTGAAAA
*
599884 TTTTTGAAAATAT
62 ATTTTGAAAATAT
* *
599897 ATTTATATTATATAGTTTTTGAAAATATTTTTG--AATATATATA-TATATAGTTTT-AAAACAT
1 ATATATAATATATAGTTTTTGAAAATA-TTTTGAAAATATATATATTATATAGTTTTGAAAA-AT
599958 TTTGAAAATAT
64 TTTGAAAATAT
* * * * *
599969 ATATATAATCTATAGTTTTTTAAAATATTTTGAAAATATATATAATATATATTTTTGAAAATGTT
1 ATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATATTATATAGTTTTGAAAA-ATT
* *
600034 TTTAAAAAAT
65 TTGAAAATAT
* ** * *
600044 GTATATAATATATAG-TTTTGAATTTTTTTTGAAAA-ATATATATTATATAGTTTTAAAAAAATA
1 ATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATATTATATAGTTTT---GAAA-A
600107 ATTTTTGAAAATAT
62 A-TTTTGAAAATAT
* * ** *
600121 AT-TAT--TATAT-G-TTTTGAAAACAATTTTCAAAA-ACGTATATAATATAGTTTT-AAAAATT
1 ATATATAATATATAGTTTTTGAAAA-TATTTTGAAAATATATATATTATATAGTTTTGAAAAATT
600179 ATTTTTATTT
Statistics
Matches: 235, Mismatches: 33, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
68 2 0.01
69 2 0.01
70 3 0.01
71 9 0.04
72 46 0.20
73 45 0.19
74 56 0.24
75 28 0.12
76 23 0.10
77 21 0.09
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (74 bp):
ATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATATTATATAGTTTTGAAAAATTT
TGAAAATAT
Found at i:600204 original size:16 final size:16
Alignment explanation
Indices: 600176--600229 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
600166 AGTTTTAAAA
600176 ATTATT-TTTATTTTT
1 ATTATTATTTATTTTT
600191 ATTA-TATATTA-TTTT
1 ATTATTAT-TTATTTTT
*
600206 AATATTATTTATTTTT
1 ATTATTATTTATTTTT
600222 ATT-TTATT
1 ATTATTATT
600230 AATATTCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 12 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTATTATTTATTTTT
Found at i:600227 original size:11 final size:11
Alignment explanation
Indices: 600176--600235 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
600166 AGTTTTAAAA
600176 ATTATTTTTATT
1 ATTA-TTTTATT
* *
600188 TTTATTATA-T
1 ATTATTTTATT
*
600198 ATTATTTTAAT
1 ATTATTTTATT
600209 ATTA-TTTATT
1 ATTATTTTATT
*
600219 TTTATTTTATT
1 ATTATTTTATT
*
600230 AATATT
1 ATTATT
600236 CTCTTTTCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
10 16 0.42
11 19 0.50
12 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:601418 original size:24 final size:22
Alignment explanation
Indices: 601362--601431 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
601352 GTCCTTTAAA
601362 TTTTTAGTTATTCATTTTTTCC
1 TTTTTAGTTATTCATTTTTTCC
* *
601384 TTTTTA-ATATTATCATTTTTT-T
1 TTTTTAGTTA-T-TCATTTTTTCC
601406 TATTTTAGTTATTCATTTTTT-C
1 T-TTTTAGTTATTCATTTTTTCC
601428 TTTT
1 TTTT
601432 AATTTTAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 5 0.12
22 18 0.45
23 15 0.38
24 2 0.05
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTTTAGTTATTCATTTTTTCC
Found at i:601448 original size:43 final size:45
Alignment explanation
Indices: 601363--601453 Score: 134
Period size: 43 Copynumber: 2.1 Consensus size: 45
601353 TCCTTTAAAT
*
601363 TTTTAGTTATTCATTTTTTCCTTTTTAATATTATCATTTTTTTTA
1 TTTTAGTTATTCATTTTTTCCTTTTTAATATTATCATGTTTTTTA
*
601408 TTTTAGTTATTCATTTTTT-C-TTTTAATTTTAGT-ATGTTTTTTA
1 TTTTAGTTATTCATTTTTTCCTTTTTAATATTA-TCATGTTTTTTA
601451 TTT
1 TTT
601454 GTTTTGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 22 0.51
44 2 0.05
45 19 0.44
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (45 bp):
TTTTAGTTATTCATTTTTTCCTTTTTAATATTATCATGTTTTTTA
Found at i:601601 original size:24 final size:25
Alignment explanation
Indices: 601552--601605 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
601542 ATTTATTTAA
* *
601552 TATTTTTTTATTTTTTCCTTTGATT
1 TATTTTTTTATTTTTTCCATTAATT
601577 TATTTTTTT-TTATTTT-CATTAATT
1 TATTTTTTTATT-TTTTCCATTAATT
601601 TATTT
1 TATTT
601606 AATATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (25 bp):
TATTTTTTTATTTTTTCCATTAATT
Found at i:602697 original size:20 final size:22
Alignment explanation
Indices: 602655--602699 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
602645 TCTCATTAAC
* *
602655 TTTTTCTTTTTATTCTTTCATT
1 TTTTTCTTCTTATTATTTCATT
602677 TTTTTCTTCTT-TTATTT-ATT
1 TTTTTCTTCTTATTATTTCATT
602697 TTT
1 TTT
602700 ATCATTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCTTCTTATTATTTCATT
Found at i:604767 original size:150 final size:144
Alignment explanation
Indices: 604501--604782 Score: 402
Period size: 150 Copynumber: 1.9 Consensus size: 144
604491 AAAGTCGATA
*
604501 CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAACAGGTGGGCT
1 CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAACAGGAGGGCT
* *
604566 TCCATAAATGTAATCTGAGACTGGCCCGTGGGTTTAAGAATAGATGGGGCAGATACAGCCTTGAA
66 TCCATAAATGTAATCCGAGACTGGCCAGTGGGTTTAAGAATAGATGGGGCAGATACAGCCTTGAA
604631 GAATCCTTAAACTG
131 GAATCCTTAAACTG
* *
604645 CTTCAACAGAGAATTCTTGTAAAGAACATAAGGCGCGAAAGGATGGAAAAGGAAATCCAAGCAGA
1 CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAA--C-AG--G-
* * * * * **
604710 AGTGCTTCCATGAATGTAATCCGAGACTGTCCAGTGGGTTTAAGAATGGATGGGGCAGTTGTAGC
60 AGGGCTTCCATAAATGTAATCCGAGACTGGCCAGTGGGTTTAAGAATAGATGGGGCAGATACAGC
604775 CTTGAAGA
125 CTTGAAGA
604783 CGCCTCAAAC
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
144 53 0.44
146 1 0.01
147 2 0.02
149 1 0.01
150 63 0.52
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (144 bp):
CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAACAGGAGGGCT
TCCATAAATGTAATCCGAGACTGGCCAGTGGGTTTAAGAATAGATGGGGCAGATACAGCCTTGAA
GAATCCTTAAACTG
Found at i:605817 original size:99 final size:99
Alignment explanation
Indices: 605710--605915 Score: 351
Period size: 99 Copynumber: 2.1 Consensus size: 99
605700 ATTATAATAT
*
605710 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCC-AGCTTTATGG
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCCGA-CTTTATGG
* *
605774 ATAAGATTCAACTAGCCTGATAAAGGTGCTTATAA
65 ATAAGATTCAACTAGCCTGATAAAGATGATTATAA
* *
605809 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGTCTCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCCGACTTTATGGA
605874 TAAGATTCAACTAGCCTGATAAAGATGATTATAA
66 TAAGATTCAACTAGCCTGATAAAGATGATTATAA
605908 TATATATA
1 TATATATA
605916 TATATATATA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
99 100 0.99
100 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (99 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCCGACTTTATGGA
TAAGATTCAACTAGCCTGATAAAGATGATTATAA
Found at i:605914 original size:2 final size:2
Alignment explanation
Indices: 605903--605939 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
605893 TAAAGATGAT
605903 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
605940 AAGCTTGAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:610294 original size:23 final size:23
Alignment explanation
Indices: 610268--610323 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
610258 AGGTTAGAGC
*
610268 TTTGGTTTGGTCCT-GGGTTTGGG
1 TTTGGTTTGG-CCTCGAGTTTGGG
* *
610291 TTTGGTTCGGGCTCGAGTTTGGG
1 TTTGGTTTGGCCTCGAGTTTGGG
610314 TTTGGTTTGG
1 TTTGGTTTGG
610324 GTATTGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.02, C:0.09, G:0.43, T:0.46
Consensus pattern (23 bp):
TTTGGTTTGGCCTCGAGTTTGGG
Found at i:610333 original size:23 final size:22
Alignment explanation
Indices: 610283--610338 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
610273 TTTGGTCCTG
*
610283 GGTTTGGGTTTGGTTCGGGCTC
1 GGTTTGGGTTTGGTTCGGGATC
* *
610305 GAGTTTGGGTTTGGTTTGGGTATT
1 G-GTTTGGGTTTGGTTCGGG-ATC
610329 GGTTTTGGGT
1 GG-TTTGGGT
610339 ATTTTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.04
23 18 0.64
24 9 0.32
ACGTcount: A:0.04, C:0.05, G:0.45, T:0.46
Consensus pattern (22 bp):
GGTTTGGGTTTGGTTCGGGATC
Found at i:610337 original size:13 final size:12
Alignment explanation
Indices: 610307--610341 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
610297 TCGGGCTCGA
610307 GTTTGGGT-TTG
1 GTTTGGGTATTG
610318 GTTTGGGTATTG
1 GTTTGGGTATTG
610330 GTTTTGGGTATT
1 G-TTTGGGTATT
610342 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 4 0.18
13 10 0.45
ACGTcount: A:0.06, C:0.00, G:0.40, T:0.54
Consensus pattern (12 bp):
GTTTGGGTATTG
Found at i:610353 original size:3 final size:3
Alignment explanation
Indices: 610345--610397 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
610335 GGGTATTTTT
610345 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
610393 TAA TA
1 TAA TA
610398 TAAGAGTTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:610946 original size:159 final size:159
Alignment explanation
Indices: 610717--611137 Score: 585
Period size: 160 Copynumber: 2.6 Consensus size: 159
610707 CTCCTTACGT
* *
610717 GATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCTA-ATT
1 GATGG-AT-GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCAT-TAGATG
* * * * *
610781 ATTTATTCTCATTATGAACTCTCTCGTTGGAAATGTTATTCACCTCATTCTGTGATGGAATCGAA
63 AGTTATTCTCATTATGAACTCTCCCATTGGAAATGTTATCCACCTCATTCTGTGATGGAATCAAA
* **
610846 -CAAAGTGATGATGTTGATCCAACTTTATATGC
128 TCAAAG-GATGATGCTGATCCAACTCCATATGC
* * * * *
610878 TATGGATGAGCCAAGGTTAAACAAGTTCTTCTTATTATGAACTTCTTATCCCTTATTAGATGAGT
1 GATGGATGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTAGATGAGT
* * * *
610943 TATTCTCATTATGAAGTCTCCCATTGGAAATATTGATCCACCTCCTTCTGTGATGGATTCAAATC
66 TATTCTCATTATGAACTCTCCCATTGGAAATGTT-ATCCACCTCATTCTGTGATGGAATCAAATC
*
611008 AAAGGTTGATGCTGATCCAACTCCATATGC
130 AAAGGATGATGCTGATCCAACTCCATATGC
*
611038 GATGGATGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGT
1 GATGGATGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTAGATGAGT
*
611103 TTTTCTCATTATGAACTCTCCCATTGGAAATGTTA
66 TATTCTCATTATGAACTCTCCCATTGGAAATGTTA
611138 ATTGGTTTAT
Statistics
Matches: 228, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
158 2 0.01
159 79 0.35
160 138 0.61
161 9 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (159 bp):
GATGGATGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTAGATGAGT
TATTCTCATTATGAACTCTCCCATTGGAAATGTTATCCACCTCATTCTGTGATGGAATCAAATCA
AAGGATGATGCTGATCCAACTCCATATGC
Found at i:615065 original size:32 final size:32
Alignment explanation
Indices: 615024--615085 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
615014 AAATTGAATA
* * *
615024 GTGAACAGTGTAACGATGCACTGTTACAGTCC
1 GTGAACAGTGCAACGATACACTATTACAGTCC
*
615056 GTGAACAGTGCATCGATACACTATTACAGT
1 GTGAACAGTGCAACGATACACTATTACAGT
615086 ACTGCTACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (32 bp):
GTGAACAGTGCAACGATACACTATTACAGTCC
Found at i:615735 original size:56 final size:58
Alignment explanation
Indices: 615674--615834 Score: 209
Period size: 59 Copynumber: 2.8 Consensus size: 58
615664 ATGCCCTATC
***
615674 TGGAAATCCATATTTTTAATATGATTT-TTATCA-TTTAGCACACTCAGTGCTCCATA
1 TGGAAATCCATACACTTAATATGATTTCTTATCATTTTAGCACACTCAGTGCTCCATA
* * *
615730 TGGAAATCTATACACTTAGTATGATTTCCTTATCATTTTAGCACAGTCAGTGCTCCATA
1 TGGAAATCCATACACTTAATATGATTT-CTTATCATTTTAGCACACTCAGTGCTCCATA
* * *
615789 TGGAAATCTATACACTCAGTATGATTTCCTTATCATTTTAGCACAC
1 TGGAAATCCATACACTTAATATGATTT-CTTATCATTTTAGCACAC
615835 AAAGTGCCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
56 22 0.23
58 6 0.06
59 66 0.70
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (58 bp):
TGGAAATCCATACACTTAATATGATTTCTTATCATTTTAGCACACTCAGTGCTCCATA
Found at i:615841 original size:59 final size:59
Alignment explanation
Indices: 615693--615834 Score: 245
Period size: 59 Copynumber: 2.5 Consensus size: 59
615683 ATATTTTTAA
*
615693 TATGATTT--TTATCA-TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTTAG
1 TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAG
*
615749 TATGATTTCCTTATCATTTTAGCACAGTCAGTGCTCCATATGGAAATCTATACACTCAG
1 TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAG
615808 TATGATTTCCTTATCATTTTAGCACAC
1 TATGATTTCCTTATCATTTTAGCACAC
615835 AAAGTGCCAT
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
56 8 0.10
58 6 0.08
59 66 0.82
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (59 bp):
TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAG
Found at i:615861 original size:59 final size:58
Alignment explanation
Indices: 615584--615842 Score: 208
Period size: 59 Copynumber: 4.5 Consensus size: 58
615574 GTATGCTTCC
* * * *
615584 CCTT-TCATTTTAGCACACAAAGTACCC-TATTCGAAAGTCCATAC-CATTAGTATGATTT
1 CCTTATCATTTTAGCACACAAAGTGCCCATA-TGGAAA-TCTATACAC-TCAGTATGATTT
** * * * * * *** * *
615642 TGTTACCGTTTTAGCACATAATA-TGCCCTATCTGGAAATCCATATTTTTAATATGATTT
1 CCTTATCATTTTAGCACACAA-AGTGCCC-ATATGGAAATCTATACACTCAGTATGATTT
** *
615701 --TTATCA-TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTTAGTATGATTT
1 CCTTATCATTTTAGCACACAAAGTGC-CCATATGGAAATCTATACACTCAGTATGATTT
***
615757 CCTTATCATTTTAGCACAGTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTT
1 CCTTATCATTTTAGCACACAAAGTGC-CCATATGGAAATCTATACACTCAGTATGATTT
615816 CCTTATCATTTTAGCACACAAAGTGCC
1 CCTTATCATTTTAGCACACAAAGTGCC
615843 ATTCGGTAAT
Statistics
Matches: 164, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
55 1 0.01
56 36 0.22
57 6 0.04
58 9 0.05
59 105 0.64
60 6 0.04
61 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (58 bp):
CCTTATCATTTTAGCACACAAAGTGCCCATATGGAAATCTATACACTCAGTATGATTT
Found at i:616280 original size:17 final size:18
Alignment explanation
Indices: 616238--616280 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
616228 ATCTTAAGGG
*
616238 AGTGCATCGATACACTACC
1 AGTGCATAGATACACTA-C
*
616257 TGTGCATAGATACACT-C
1 AGTGCATAGATACACTAC
616274 AGTGCAT
1 AGTGCAT
616281 TCGATGCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
19 14 0.67
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (18 bp):
AGTGCATAGATACACTAC
Found at i:622906 original size:59 final size:58
Alignment explanation
Indices: 622752--622899 Score: 224
Period size: 59 Copynumber: 2.5 Consensus size: 58
622742 ATCCATATTT
*
622752 TCAATATGATTTCCTTATCATTTAGTACACTCAGTGCTCCATATGGAAATATATACAC
1 TCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATATATACAC
* * *
622810 TCAGTATGATTTCCTTATCAGTTTAGCACACTCAGTGCTCCATATGTAAATCTATACAC
1 TCAATATGATTTCCTTATCA-TTTAGCACACTCAGTGCTCCATATGGAAATATATACAC
* *
622869 TCAATATGTTTTCCTTATTATTTTAGCACAC
1 TCAATATGATTTCCTTATCA-TTTAGCACAC
622900 AAAGTGCCAT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 19 0.23
59 62 0.77
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (58 bp):
TCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATATATACAC
Found at i:623345 original size:17 final size:18
Alignment explanation
Indices: 623303--623345 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
623293 ATCTTAAGAG
*
623303 AGTGCATCGATACACTACC
1 AGTGCATAGATACACTA-C
*
623322 TGTGCATAGATACACT-C
1 AGTGCATAGATACACTAC
623339 AGTGCAT
1 AGTGCAT
623346 TCGATGCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
19 14 0.67
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (18 bp):
AGTGCATAGATACACTAC
Found at i:628961 original size:17 final size:17
Alignment explanation
Indices: 628939--628976 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
628929 GACCTAAGAG
*
628939 TAAATCTTA-GAACATAA
1 TAAATCTAAGGAACA-AA
628956 TAAATCTAAGGAACAAA
1 TAAATCTAAGGAACAAA
628973 TAAA
1 TAAA
628977 AAAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (17 bp):
TAAATCTAAGGAACAAA
Found at i:630458 original size:22 final size:22
Alignment explanation
Indices: 630433--630493 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
630423 TCTCACTCTC
*
630433 TCCGGCGACATCCGTTCCTATA
1 TCCGACGACATCCGTTCCTATA
630455 TCCGACGACATCCGTTCCTATA
1 TCCGACGACATCCGTTCCTATA
630477 TCCGACGACATCC-TTCC
1 TCCGACGACATCCGTTCC
630494 CCATCTCTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 4 0.11
22 34 0.89
ACGTcount: A:0.20, C:0.39, G:0.15, T:0.26
Consensus pattern (22 bp):
TCCGACGACATCCGTTCCTATA
Found at i:631149 original size:12 final size:12
Alignment explanation
Indices: 631128--631161 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
631118 ACCACATTTC
*
631128 CAATACCAAACA
1 CAATATCAAACA
631140 CAATATCAAACA
1 CAATATCAAACA
*
631152 CAATCTCAAA
1 CAATATCAAA
631162 ATCCACTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:631322 original size:24 final size:24
Alignment explanation
Indices: 631287--631364 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
631277 GTATTCAAAA
* *
631287 TTTGATCATGGTTAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
*
631311 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
631335 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
631359 TTTGAT
1 TTTGAT
631365 GATGTTTCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:631584 original size:3 final size:3
Alignment explanation
Indices: 631570--631598 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
631560 AGAAGTCCCC
631570 GAA GAA -AA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
631599 AGAGCCACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:633666 original size:18 final size:18
Alignment explanation
Indices: 633643--633678 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
633633 AAGCAAAAGG
*
633643 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
633661 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
633679 CAACCGCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:633983 original size:20 final size:20
Alignment explanation
Indices: 633960--634016 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
633950 CCATATTCGC
*
633960 AACTCGAATTCCAAATTTAA
1 AACTCGAATTCCAAATTGAA
* * *
633980 AACTCAAATTTCCAACTCGAA
1 AACTCGAA-TTCCAAATTGAA
*
634001 AA-TCGAATTCCTAATT
1 AACTCGAATTCCAAATT
634017 CGAAGCTCAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
19 6 0.21
20 11 0.39
21 11 0.39
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (20 bp):
AACTCGAATTCCAAATTGAA
Found at i:634026 original size:40 final size:40
Alignment explanation
Indices: 633963--634045 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
633953 TATTCGCAAC
* *
633963 TCGAATTCCAAATTTAAAACTCAAATTTC-CAACTCGAAAA
1 TCGAATTCCAAATTCAAAACTCAAA-TTCGCAACACGAAAA
* * *
634003 TCGAATTCCTAATTCGAAGCTCAAATTCGCAACACGAAAA
1 TCGAATTCCAAATTCAAAACTCAAATTCGCAACACGAAAA
634043 TCG
1 TCG
634046 CAACTTGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.08
40 34 0.92
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (40 bp):
TCGAATTCCAAATTCAAAACTCAAATTCGCAACACGAAAA
Found at i:634075 original size:20 final size:20
Alignment explanation
Indices: 634039--634113 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
634029 TCGCAACACG
*
634039 AAAA-TCGCAACTTGATATT
1 AAAATTCGCAACTCGATATT
*
634058 AAAATTCGTAACTCGATATT
1 AAAATTCGCAACTCGATATT
* * *
634078 AAAATTTGCAACTCGAAAAT
1 AAAATTCGCAACTCGATATT
*
634098 ATAATTCGCAACTCGA
1 AAAATTCGCAACTCGA
634114 AATCGATTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 4 0.09
20 43 0.91
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (20 bp):
AAAATTCGCAACTCGATATT
Found at i:634197 original size:34 final size:34
Alignment explanation
Indices: 634159--634231 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
634149 TAAATATCCT
*
634159 GTTGCGATTTTCGTGTTGCGAATTCGATTTTTGA
1 GTTGCGATTTTCGTGTTGCAAATTCGATTTTTGA
*
634193 GTTGCGATTTTCGTGTTGCAAATTTGATTTTTGA
1 GTTGCGATTTTCGTGTTGCAAATTCGATTTTTGA
*
634227 ATTGC
1 GTTGC
634232 TAAATCGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.16, C:0.11, G:0.25, T:0.48
Consensus pattern (34 bp):
GTTGCGATTTTCGTGTTGCAAATTCGATTTTTGA
Found at i:634223 original size:20 final size:20
Alignment explanation
Indices: 634198--634303 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 20
634188 TTTGAGTTGC
*
634198 GATTTTCGTGTTGCAAATTT
1 GATTTTCGAGTTGCAAATTT
* * *
634218 GATTTTTGAATTGCTAAA-TC
1 GATTTTCGAGTTGC-AAATTT
* *
634238 GATTTTTGCA-TTGCGAATTT
1 GATTTTCG-AGTTGCAAATTT
* *
634258 -AATTTCGAGTTGCGAATTT
1 GATTTTCGAGTTGCAAATTT
* *
634277 GAATATCGAGTTGCAAATTT
1 GATTTTCGAGTTGCAAATTT
634297 GATTTTC
1 GATTTTC
634304 TTAAAGGTAG
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
19 17 0.25
20 47 0.68
21 4 0.06
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.45
Consensus pattern (20 bp):
GATTTTCGAGTTGCAAATTT
Found at i:636111 original size:21 final size:21
Alignment explanation
Indices: 636087--636126 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
636077 TTGATATAGT
* *
636087 ATGGAATGTGGATCTTGAATG
1 ATGGAAGGTGGATCCTGAATG
*
636108 ATGGGAGGTGGATCCTGAA
1 ATGGAAGGTGGATCCTGAA
636127 CGATTGGAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGGAAGGTGGATCCTGAATG
Found at i:636135 original size:21 final size:21
Alignment explanation
Indices: 636094--636226 Score: 76
Period size: 21 Copynumber: 6.3 Consensus size: 21
636084 AGTATGGAAT
* * *
636094 GTGGATCTTGAATGATGGGAG
1 GTGGATCCTGAACGATTGGAG
636115 GTGGATCCTGAACGATTGGAG
1 GTGGATCCTGAACGATTGGAG
* *
636136 G-GGCCTCTTGAACGA-TGAGAG
1 GTGG-ATCCTGAACGATTG-GAG
* * *
636157 G-GGCCTCTTAAACGA-TGAGAG
1 GTGG-ATCCTGAACGATTG-GAG
* * * *
636178 GTGAATTCTGAACAATGGGAG
1 GTGGATCCTGAACGATTGGAG
* *
636199 GTGGATCCTGAACAATTGTAG
1 GTGGATCCTGAACGATTGGAG
636220 GTGGATC
1 GTGGATC
636227 AGGCTTCTTC
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.04
21 85 0.93
22 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (21 bp):
GTGGATCCTGAACGATTGGAG
Found at i:636534 original size:21 final size:21
Alignment explanation
Indices: 636510--636700 Score: 120
Period size: 21 Copynumber: 9.1 Consensus size: 21
636500 TGAAATAATC
*
636510 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* * *
636531 TCACGTAAAGCATCTAACTTA
1 TCACGTAAAGCACCTACCTCA
* **
636552 CCACGTAAAGCACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
* **
636573 TCACGTAAAACAATTACCTCA
1 TCACGTAAAGCACCTACCTCA
*
636594 CCACGTAAAG-ACCCTACCTCA
1 TCACGTAAAGCA-CCTACCTCA
** * **
636615 TCACGCCATGCACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
636636 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
** *
636657 TCATATAAAGCA-TTAACCTCA
1 TCACGTAAAGCACCT-ACCTCA
* *
636678 TCATGTAAAGCACCTAACTCA
1 TCACGTAAAGCACCTACCTCA
636699 TC
1 TC
636701 TCGTGAAGGT
Statistics
Matches: 125, Mismatches: 37, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.02
21 118 0.94
22 4 0.03
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:636676 original size:63 final size:63
Alignment explanation
Indices: 636510--636691 Score: 179
Period size: 63 Copynumber: 2.9 Consensus size: 63
636500 TGAAATAATC
* * * *
636510 TCACGTAGAGCACCTACCTCATCACGTAAAGCATCTAA-CTTACCACGTAAAGCACCATTGTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCAT-TAACCTCATCACGCAAAGCACCATTGTCA
* ** * ** * *
636573 TCACGTAAAACAATTACCTCACCACGTAAAGACCCT-ACCTCATCACGCCATGCACCATTGTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAG-CATTAACCTCATCACGCAAAGCACCATTGTCA
* ** * *
636636 TCACGTAAAGCACCGACCTCATCATATAAAGCATTAACCTCATCATGTAAAGCACC
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCATTAACCTCATCACGCAAAGCACC
636692 TAACTCATCT
Statistics
Matches: 91, Mismatches: 25, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
62 3 0.03
63 87 0.96
64 1 0.01
ACGTcount: A:0.35, C:0.33, G:0.11, T:0.21
Consensus pattern (63 bp):
TCACGTAAAGCACCTACCTCATCACGTAAAGCATTAACCTCATCACGCAAAGCACCATTGTCA
Found at i:636965 original size:42 final size:42
Alignment explanation
Indices: 636800--636965 Score: 178
Period size: 42 Copynumber: 4.0 Consensus size: 42
636790 GTGATGGAAT
* * * *
636800 AGGTGATGGATCTCTGTGTCGAGGTGTAGAGTCGAAT--A-G
1 AGGTGATGGATCTCAGTGTCGAAGTGTAGAATCGACTCGATG
* * * * *
636839 AGGTAATGGCTCTCAGTGTCGAGGTGTAGAATCGGCTCGATC
1 AGGTGATGGATCTCAGTGTCGAAGTGTAGAATCGACTCGATG
* *
636881 AGGTGATGGATCTCAGTGTCAAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCAGTGTCGAAGTGTAGAATCGACTCGATG
* *
636923 AGGTGATGGATCTC-GATGTCGAAGTGAAGAATCGACTTGATG
1 AGGTGATGGATCTCAG-TGTCGAAGTGTAGAATCGACTCGATG
636965 A
1 A
636966 AAAAATGGGG
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 31 0.29
41 2 0.02
42 73 0.69
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCAGTGTCGAAGTGTAGAATCGACTCGATG
Found at i:638489 original size:15 final size:15
Alignment explanation
Indices: 638471--638503 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
638461 CTTGAAACTT
638471 AAATTCACAACACGA
1 AAATTCACAACACGA
*
638486 AAA-TCGCAACACGA
1 AAATTCACAACACGA
638500 AAAT
1 AAAT
638504 GAAATTCGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.55, C:0.24, G:0.09, T:0.12
Consensus pattern (15 bp):
AAATTCACAACACGA
Found at i:638512 original size:20 final size:20
Alignment explanation
Indices: 638484--638553 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
638474 TTCACAACAC
*
638484 GAAAATCGCAACACGAAAAT
1 GAAATTCGCAACACGAAAAT
*
638504 GAAATTCGCAGCACG---A-
1 GAAATTCGCAACACGAAAAT
*
638520 -AAA-TCGCAACTCGAAAAT
1 GAAATTCGCAACACGAAAAT
638538 GAAATTCGCAACACGA
1 GAAATTCGCAACACGA
638554 TTTTTGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
14 8 0.21
15 3 0.08
17 2 0.05
19 3 0.08
20 23 0.59
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAATTCGCAACACGAAAAT
Found at i:638519 original size:34 final size:34
Alignment explanation
Indices: 638471--638553 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
638461 CTTGAAACTT
*
638471 AAATTCACAACACGAAAATCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATCGCAACACGAAAATG
* *
638505 AAATTCGCAGCACGAAAATCGCAACTCGAAAATG
1 AAATTCGCAACACGAAAATCGCAACACGAAAATG
638539 AAATTCGCAACACGA
1 AAATTCGCAACACGA
638554 TTTTTGTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.13
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCGCAACACGAAAATG
Found at i:638609 original size:34 final size:34
Alignment explanation
Indices: 638571--638635 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
638561 TTTCGCGTTC
* *
638571 CGAATTTTATTTTCGCGTTGTGATTTTCGTGCTG
1 CGAATTTCATTTTCGAGTTGTGATTTTCGTGCTG
638605 CGAATTTCATTTTCGAGTTGTGATTTTCGTG
1 CGAATTTCATTTTCGAGTTGTGATTTTCGTG
638636 TTACAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (34 bp):
CGAATTTCATTTTCGAGTTGTGATTTTCGTGCTG
Found at i:638645 original size:34 final size:34
Alignment explanation
Indices: 638573--638645 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
638563 TCGCGTTCCG
* * * *
638573 AATTTTATTTTCGCGTTGTGATTTTCGTGCTGCG
1 AATTTCATTTTCGAGTTGTGATTTTCGTGCTACA
*
638607 AATTTCATTTTCGAGTTGTGATTTTCGTGTTACA
1 AATTTCATTTTCGAGTTGTGATTTTCGTGCTACA
638641 AATTT
1 AATTT
638646 AAGTTTCAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.18, C:0.12, G:0.19, T:0.51
Consensus pattern (34 bp):
AATTTCATTTTCGAGTTGTGATTTTCGTGCTACA
Found at i:639360 original size:20 final size:20
Alignment explanation
Indices: 639317--639384 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
639307 TTTACTTTTG
* *
639317 TGTTGCGAATTTGGAAA-CTG
1 TGTTGCGAAATTGGAAATC-A
**
639337 TGTTGCGAAATTGGAGTTCA
1 TGTTGCGAAATTGGAAATCA
*
639357 TGTTGC-AAATTTGAAATCA
1 TGTTGCGAAATTGGAAATCA
639376 TGTTGCGAA
1 TGTTGCGAA
639385 TTCATTGGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 16 0.41
20 22 0.56
21 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.35
Consensus pattern (20 bp):
TGTTGCGAAATTGGAAATCA
Found at i:639901 original size:6 final size:6
Alignment explanation
Indices: 639890--639972 Score: 84
Period size: 6 Copynumber: 14.3 Consensus size: 6
639880 TTGGGCCCGT
* * * *
639890 GTTTGG GTTTGG GTTTGG GTTTGG G-TT-G GTTCGG GCTCGA GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
*
639936 GTTT-G GTTTGG GTATTGG GTTTGA GTTT-G GTTTGG GT
1 GTTTGG GTTTGG GT-TTGG GTTTGG GTTTGG GTTTGG GT
639973 ATTTTGTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
4 2 0.03
5 12 0.19
6 44 0.69
7 6 0.09
ACGTcount: A:0.04, C:0.04, G:0.46, T:0.47
Consensus pattern (6 bp):
GTTTGG
Found at i:639934 original size:40 final size:40
Alignment explanation
Indices: 639875--639956 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
639865 GGTTAGGGCT
* *
639875 TTGGTTTGGGCCCGTGTTTGGGTTTGGGTTTGGGT-TTGGG
1 TTGGTTCGGGCCCGAGTTTGGGTTT-GGTTTGGGTATTGGG
*
639915 TTGGTTCGGGCTCGAGTTTGGGTTTGGTTTGGGTATTGGG
1 TTGGTTCGGGCCCGAGTTTGGGTTTGGTTTGGGTATTGGG
639955 TT
1 TT
639957 TGAGTTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 9 0.24
40 29 0.76
ACGTcount: A:0.02, C:0.07, G:0.45, T:0.45
Consensus pattern (40 bp):
TTGGTTCGGGCCCGAGTTTGGGTTTGGTTTGGGTATTGGG
Found at i:639987 original size:3 final size:3
Alignment explanation
Indices: 639979--640045 Score: 62
Period size: 3 Copynumber: 21.0 Consensus size: 3
639969 GGGTATTTTG
* * *
639979 TAA TAA TAAA TAAA TAA TAA TATT TTA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA T-AA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
640027 TAT TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TA-A TAA
640046 GAGTTGAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 42 0.79
4 11 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:640010 original size:27 final size:29
Alignment explanation
Indices: 639972--640045 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 29
639962 TTGGTTTGGG
*
639972 TATTTTGTAATAATAAATAA-A-TAATAA
1 TATTTTATAATAATAAATAATATTAATAA
639999 TATTTTATAATAAT-AATAATATTAATAA
1 TATTTTATAATAATAAATAATATTAATAA
* *
640027 TA-TTAATAATAATATATAA
1 TATTTTATAATAATAAATAA
640046 GAGTTGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.12
27 24 0.59
28 12 0.29
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
TATTTTATAATAATAAATAATATTAATAA
Found at i:644686 original size:13 final size:13
Alignment explanation
Indices: 644668--644692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
644658 TTTTCTAACC
644668 ATTTTTATTTATT
1 ATTTTTATTTATT
644681 ATTTTTATTTAT
1 ATTTTTATTTAT
644693 GTGTTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTATTTATT
Found at i:645308 original size:13 final size:13
Alignment explanation
Indices: 645289--645333 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
645279 TCGAAAGAAA
645289 AGAAAAAATAAGAG
1 AGAAAAAA-AAGAG
*
645303 AGAAAAAGAACGA-
1 AGAAAAA-AAAGAG
645316 AGAAAAAAAAGAG
1 AGAAAAAAAAGAG
645329 AGAAA
1 AGAAA
645334 GGAAGAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.15
13 12 0.44
14 10 0.37
15 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (13 bp):
AGAAAAAAAAGAG
Found at i:645334 original size:24 final size:23
Alignment explanation
Indices: 645281--645334 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 23
645271 GGAAAAAGTC
645281 GAAAGAAAAGAAAAAATAAGAGA
1 GAAAGAAAAGAAAAAATAAGAGA
645304 GAAAAAGAACGAAGAAAAAA-AAGAGA
1 G--AAAGAA--AAGAAAAAATAAGAGA
645330 GAAAG
1 GAAAG
645335 GAAGAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
23 1 0.04
24 4 0.15
25 6 0.22
26 7 0.26
27 9 0.33
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (23 bp):
GAAAGAAAAGAAAAAATAAGAGA
Found at i:645346 original size:26 final size:25
Alignment explanation
Indices: 645282--645333 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
645272 GAAAAAGTCG
645282 AAAGAAAAGAAAAAATAAGAGAGAA
1 AAAGAAAAGAAAAAATAAGAGAGAA
645307 AAAGAACGAAGAAAAAA-AAGAGAGAA
1 AAAGAA--AAGAAAAAATAAGAGAGAA
645333 A
1 A
645334 GGAAGAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 10 0.40
27 9 0.36
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (25 bp):
AAAGAAAAGAAAAAATAAGAGAGAA
Found at i:647731 original size:4 final size:4
Alignment explanation
Indices: 647722--647750 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
647712 ACTCTATCCT
647722 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
647751 ATTTTAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:650686 original size:16 final size:16
Alignment explanation
Indices: 650628--650668 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
650618 CATCACTTAT
650628 AATGCATCACCAATAA
1 AATGCATCACCAATAA
650644 AATGCATCACCAATAA
1 AATGCATCACCAATAA
650660 AATGCATCA
1 AATGCATCA
650669 TTACCAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (16 bp):
AATGCATCACCAATAA
Found at i:657611 original size:9 final size:9
Alignment explanation
Indices: 657594--657648 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
657584 TATTATACTT
657594 GAAAAAAAA
1 GAAAAAAAA
657603 GAAAGAAAAA
1 GAAA-AAAAA
657613 TGAAAAATGAAA
1 -GAAAAA--AAA
657625 -AAGAAAAAA
1 GAA-AAAAAA
657634 G-AAAAAAA
1 GAAAAAAAA
657642 GAAAAAA
1 GAAAAAA
657649 TAAATAAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.18
9 13 0.33
10 9 0.23
11 7 0.18
12 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.04
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:657618 original size:20 final size:20
Alignment explanation
Indices: 657593--657645 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
657583 ATATTATACT
657593 TGAAAAAAAAGAAAGAAAAA
1 TGAAAAAAAAGAAAGAAAAA
*
657613 TGAAAAATGAA-AAAGAAAAA
1 TGAAAAA-AAAGAAAGAAAAA
*
657633 AG-AAAAAAAGAAA
1 TGAAAAAAAAGAAA
657646 AAATAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 7 0.25
20 17 0.61
21 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (20 bp):
TGAAAAAAAAGAAAGAAAAA
Found at i:657640 original size:7 final size:7
Alignment explanation
Indices: 657594--657648 Score: 60
Period size: 7 Copynumber: 8.0 Consensus size: 7
657584 TATTATACTT
657594 GAAAAAA
1 GAAAAAA
*
657601 -AAGAAA
1 GAAAAAA
*
657607 GAAAAAT
1 GAAAAAA
*
657614 GAAAAAT
1 GAAAAAA
657621 G-AAAAA
1 GAAAAAA
657627 GAAAAAA
1 GAAAAAA
657634 GAAAAAAA
1 G-AAAAAA
657642 GAAAAAA
1 GAAAAAA
657649 TAAATAAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 10 0.24
7 24 0.59
8 7 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.04
Consensus pattern (7 bp):
GAAAAAA
Found at i:657646 original size:13 final size:13
Alignment explanation
Indices: 657594--657639 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
657584 TATTATACTT
657594 GAAAAA-AAAGAAA
1 GAAAAAGAAA-AAA
*
657607 GAAAAATGAAAAAT
1 GAAAAA-GAAAAAA
657621 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
657634 GAAAAA
1 GAAAAA
657640 AAGAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.62
14 8 0.28
15 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (13 bp):
GAAAAAGAAAAAA
Found at i:657646 original size:27 final size:27
Alignment explanation
Indices: 657593--657647 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
657583 ATATTATACT
*
657593 TGAAAAAAAAGAAAGAAAAATGAAAAA
1 TGAAAAAAAAGAAAGAAAAAAGAAAAA
657620 TGAAAAAGAAA-AAAGAAAAAAAGAAAAA
1 TGAAAAA-AAAGAAAG-AAAAAAGAAAAA
657648 ATAAATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (27 bp):
TGAAAAAAAAGAAAGAAAAAAGAAAAA
Found at i:657657 original size:15 final size:14
Alignment explanation
Indices: 657615--657657 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
657605 AAGAAAAATG
*
657615 AAAAATGAAAAAGA
1 AAAAATAAAAAAGA
*
657629 AAAAAGAAAAAAAGA
1 AAAAA-TAAAAAAGA
657644 AAAAATAAATAAAG
1 AAAAATAAA-AAAG
657658 GAGGGTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (14 bp):
AAAAATAAAAAAGA
Found at i:659731 original size:13 final size:13
Alignment explanation
Indices: 659712--659756 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
659702 TCGAAAGAAA
659712 AGAAAAAATAAGAG
1 AGAAAAAA-AAGAG
*
659726 AGAAAAAGAATGA-
1 AGAAAAA-AAAGAG
659739 AGAAAAAAAAGAG
1 AGAAAAAAAAGAG
659752 AGAAA
1 AGAAA
659757 GGAAGAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.15
13 12 0.44
14 10 0.37
15 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (13 bp):
AGAAAAAAAAGAG
Found at i:659757 original size:24 final size:23
Alignment explanation
Indices: 659704--659757 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 23
659694 GGAAAAACTC
659704 GAAAGAAAAGAAAAAATAAGAGA
1 GAAAGAAAAGAAAAAATAAGAGA
659727 GAAAAAGAATGAAGAAAAAA-AAGAGA
1 G--AAAGAA--AAGAAAAAATAAGAGA
659753 GAAAG
1 GAAAG
659758 GAAGAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
23 1 0.04
24 4 0.15
25 6 0.22
26 7 0.26
27 9 0.33
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (23 bp):
GAAAGAAAAGAAAAAATAAGAGA
Found at i:659769 original size:26 final size:25
Alignment explanation
Indices: 659705--659756 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
659695 GAAAAACTCG
659705 AAAGAAAAGAAAAAATAAGAGAGAA
1 AAAGAAAAGAAAAAATAAGAGAGAA
659730 AAAGAATGAAGAAAAAA-AAGAGAGAA
1 AAAGAA--AAGAAAAAATAAGAGAGAA
659756 A
1 A
659757 GGAAGAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 10 0.40
27 9 0.36
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (25 bp):
AAAGAAAAGAAAAAATAAGAGAGAA
Found at i:663411 original size:3 final size:3
Alignment explanation
Indices: 663403--663434 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
663393 AAATATTTAA
663403 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
663435 GTTTCAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:664133 original size:31 final size:31
Alignment explanation
Indices: 664095--664164 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
664085 CAAAGGGGGC
*
664095 GGGGCAAAGTATAATTAATCATAAAAATTGA
1 GGGGCAAAGTATAATTAAACATAAAAATTGA
664126 GGGGCAAAGTATAATTAAACATAAAAATTGA
1 GGGGCAAAGTATAATTAAACATAAAAATTGA
664157 GGGGCAAA
1 GGGGCAAA
664165 ATCAAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (31 bp):
GGGGCAAAGTATAATTAAACATAAAAATTGA
Found at i:665733 original size:6 final size:7
Alignment explanation
Indices: 665716--665740 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
665706 ACAAAAAGAG
665716 TTTTTTA
1 TTTTTTA
665723 TTTTTTA
1 TTTTTTA
665730 TTTTTTA
1 TTTTTTA
665737 TTTT
1 TTTT
665741 ATAGAAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:666156 original size:21 final size:21
Alignment explanation
Indices: 666132--666190 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
666122 TTATGGCATG
666132 TTTTCTTATGCTTTTGGC-TT
1 TTTTCTTATGCTTTTGGCGTT
* *
666152 TTTT-TTAGTTG-TTTAGGTGTT
1 TTTTCTTA--TGCTTTTGGCGTT
666173 TTTTCTTATGCTTTTGGC
1 TTTTCTTATGCTTTTGGC
666191 ATGTTTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 13 0.43
22 3 0.10
ACGTcount: A:0.07, C:0.10, G:0.19, T:0.64
Consensus pattern (21 bp):
TTTTCTTATGCTTTTGGCGTT
Found at i:666185 original size:41 final size:41
Alignment explanation
Indices: 666132--666218 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
666122 TTATGGCATG
* * *
666132 TTTTCTTATGCTTTTGGCTTTTTTTTAGTTGTTTAGGTGTT
1 TTTTCTTATGCTTTTGGCATGTTTTTAGTTGTTTAGGCGTT
666173 TTTTCTTATGCTTTTGGCATGTTTTTAGTTGTTTAGGCGTT
1 TTTTCTTATGCTTTTGGCATGTTTTTAGTTGTTTAGGCGTT
666214 TTTTC
1 TTTTC
666219 ATTTTTCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.08, C:0.09, G:0.20, T:0.63
Consensus pattern (41 bp):
TTTTCTTATGCTTTTGGCATGTTTTTAGTTGTTTAGGCGTT
Found at i:672763 original size:8 final size:8
Alignment explanation
Indices: 672745--672837 Score: 72
Period size: 8 Copynumber: 11.8 Consensus size: 8
672735 AATTTGCCTG
672745 AAAAAAG-
1 AAAAAAGA
672752 AAAAAAG-
1 AAAAAAGA
672759 -AAAAAGA
1 AAAAAAGA
672766 AAAAAAGA
1 AAAAAAGA
672774 AAGAAAA-A
1 AA-AAAAGA
*
672782 TGAAAAAATA
1 --AAAAAAGA
*
672792 TAAAAAGA
1 AAAAAAGA
672800 AAAGAAA-A
1 AAA-AAAGA
672808 AAAAGAA-A
1 AAAA-AAGA
*
672816 AAGAAAGA
1 AAAAAAGA
672824 AAAAAAGA
1 AAAAAAGA
672832 AAAAAA
1 AAAAAA
672838 AAATAATAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.08
7 10 0.14
8 42 0.58
9 11 0.15
10 3 0.04
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:672797 original size:40 final size:38
Alignment explanation
Indices: 672743--672850 Score: 116
Period size: 39 Copynumber: 2.8 Consensus size: 38
672733 ATAATTTGCC
672743 TGAAAAAAGAAAAAAGAAAAAGAAAAAAAGAAAGAA-AAA
1 TGAAAAAA-AAAAAAGAAAAAGAAAAAAAGAAA-AAGAAA
672782 TGAAAAAATATAAAAAG-AAAAGAAAAAAAAGAAAAAGAAA
1 TGAAAAAA-A-AAAAAGAAAAAG-AAAAAAAGAAAAAGAAA
*
672822 -GAAAAAAAGAAAAA-AAAAATAATAAAAAG
1 TGAAAAAAA-AAAAAGAAAAAGAA-AAAAAG
672851 GGGTTCAAGA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
37 2 0.03
38 16 0.26
39 23 0.38
40 20 0.33
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (38 bp):
TGAAAAAAAAAAAAGAAAAAGAAAAAAAGAAAAAGAAA
Found at i:672815 original size:54 final size:52
Alignment explanation
Indices: 672744--672850 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 52
672734 TAATTTGCCT
672744 GAAAAAAGAAAAAAGAAAAAGAAA-AAAAGAAAGAAAAATGAAAAA-ATATAAAAA
1 GAAAAAAGAAAAAAGAAAAAGAAAGAAAA-AAAGAAAAA--AAAAATA-ATAAAAA
672798 GAAAAGAA-AAAAAAGAAAAAGAAAGAAAAAAAGAAAAAAAAAATAATAAAAA
1 GAAAA-AAGAAAAAAGAAAAAGAAAGAAAAAAAGAAAAAAAAAATAATAAAAA
672850 G
1 G
672851 GGGTTCAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
52 13 0.26
53 1 0.02
54 30 0.60
55 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (52 bp):
GAAAAAAGAAAAAAGAAAAAGAAAGAAAAAAAGAAAAAAAAAATAATAAAAA
Found at i:672817 original size:47 final size:47
Alignment explanation
Indices: 672746--672836 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 47
672736 ATTTGCCTGA
* *
672746 AAAAAGAAAAAAGAAAAAGAAAAAAAGAAAG-AAAAATGAAAAAATAT
1 AAAAAGAAAAAAAAAAAAG-AAAAAAGAAAGAAAAAAAGAAAAAATAT
672793 AAAAAGAAAAGAAAAAAAAG-AAAAAGAAAGAAAAAAAGAAAAAA
1 AAAAAGAAAA-AAAAAAAAGAAAAAAGAAAGAAAAAAAGAAAAAA
672837 AAAATAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 10 0.25
47 22 0.55
48 8 0.20
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (47 bp):
AAAAAGAAAAAAAAAAAAGAAAAAAGAAAGAAAAAAAGAAAAAATAT
Found at i:672849 original size:1 final size:1
Alignment explanation
Indices: 672745--672840 Score: 57
Period size: 1 Copynumber: 96.0 Consensus size: 1
672735 AATTTGCCTG
* * * * * ** * * * *
672745 AAAAAAGAAAAAAGAAAAAGAAAAAAAGAAAGAAAAATGAAAAAATATAAAAAGAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
672810 AAGAAAAAGAAAGAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
672841 TAATAAAAAG
Statistics
Matches: 66, Mismatches: 29, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (1 bp):
A
Found at i:672849 original size:11 final size:11
Alignment explanation
Indices: 672745--672840 Score: 81
Period size: 12 Copynumber: 8.5 Consensus size: 11
672735 AATTTGCCTG
672745 AAAAAAGAAAAA
1 AAAAAAG-AAAA
672757 AGAAAAAGAAAA
1 A-AAAAAGAAAA
672769 AAAGAAAGAAAA
1 AAA-AAAGAAAA
* *
672781 ATGAAAA-AATA
1 A-AAAAAGAAAA
*
672792 TAAAAAG-AAA
1 AAAAAAGAAAA
*
672802 AGAAAA-AAAA
1 AAAAAAGAAAA
*
672812 GAAAAAGAAAGA
1 AAAAAAGAAA-A
672824 AAAAAAGAAAA
1 AAAAAAGAAAA
672835 AAAAAA
1 AAAAAA
672841 TAATAAAAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
10 17 0.25
11 15 0.22
12 28 0.42
13 7 0.10
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:673826 original size:16 final size:16
Alignment explanation
Indices: 673805--673844 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
673795 TTACATTCAT
673805 AAAATGCATGATGTGA
1 AAAATGCATGATGTGA
673821 AAAATGCATGATGTGA
1 AAAATGCATGATGTGA
*
673837 TAAATGCA
1 AAAATGCA
673845 ATTAAGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (16 bp):
AAAATGCATGATGTGA
Found at i:674341 original size:45 final size:45
Alignment explanation
Indices: 674283--674466 Score: 119
Period size: 45 Copynumber: 4.1 Consensus size: 45
674273 GTCTCAATTC
*
674283 AATCTTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCT
1 AATCTTCCCTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCT
* * * * ** * * * *
674328 AATCTACCCTGAAGAAGAGGCGGAGTGGATCCTCTTTTTTCAAATTT
1 AATCTTCCCTGAAGAACA-GTGGAGTGAATCAACATTTCT-AGATCT
* * ** *
674375 GATCTTCCCTGAAGAAACAGT---G-GAA-CAAGTATGCCTCGAT-T
1 AATCTTCCCTGAAG-AACAGTGGAGTGAATCAA-CATTTCTAGATCT
*
674416 CAATCTTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCT
1 -AATCTTCCCTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCT
*
674462 GATCT
1 AATCT
674467 ACTCTAAAGT
Statistics
Matches: 96, Mismatches: 32, Indels: 22
0.64 0.21 0.15
Matches are distributed among these distances:
41 7 0.07
42 15 0.16
43 4 0.04
44 2 0.02
45 29 0.30
46 19 0.20
47 17 0.18
48 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (45 bp):
AATCTTCCCTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCT
Found at i:674437 original size:134 final size:134
Alignment explanation
Indices: 674140--674612 Score: 511
Period size: 134 Copynumber: 3.5 Consensus size: 134
674130 TCAAATTGAA
* * * ** * *
674140 CTCGATTCAATATTCCTTGAAGAACAGTGGAATGAATTAACGTTTCCGGATCTGATTTTCCCTGA
1 CTCGATTCAATATTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCTGATCTACCCTGA
* * * * * * * *
674205 AGAAGCA-GCGTAACGAATCTCTTGTTTTTTTAGATTTGATCTTCCCTG-AGGATCAGTGGAACA
66 AGAAG-AGGCGGAGCGGATC-C-TCTTTTTTCAAATTTGATCTTCCCTGAAGAAACAGTGGAACA
* * *
674268 TGTCTGT
128 AGTATGC
* * *
674275 CTCAATTCAATCTTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCTAATCTACCCTGA
1 CTCGATTCAATATTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCTGATCTACCCTGA
*
674340 AGAAGAGGCGGAGTGGATCCTCTTTTTTCAAATTTGATCTTCCCTGAAGAAACAGTGGAACAAGT
66 AGAAGAGGCGGAGCGGATCCTCTTTTTTCAAATTTGATCTTCCCTGAAGAAACAGTGGAACAAGT
674405 ATGC
131 ATGC
* * *
674409 CTCGATTCAATCTTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCTGATCTACTCTAA
1 CTCGATTCAATATTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCTGATCTACCCTGA
* * * * * * *
674474 AGTAGTGACGGAGCAGATCC-CTTTTTTCTATATTTGATATTCCCTGAAGAAGCAGTGGAACAAG
66 AGAAGAGGCGGAGCGGATCCTCTTTTTTC-AAATTTGATCTTCCCTGAAGAAACAGTGGAACAAG
674538 TATGC
130 TATGC
* * * * * * * * * *
674543 CTTGATTCAATATTCCCTGAAGAATAGTGGACTGAATCAATAATTCCAGATTTGATTTACCTTGA
1 CTCGATTCAATATTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCTGATCTACCCTGA
674608 AGAAG
66 AGAAG
674613 CAGTGGAGAA
Statistics
Matches: 287, Mismatches: 48, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
133 31 0.11
134 188 0.66
135 68 0.24
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (134 bp):
CTCGATTCAATATTCCTTGAAGAACAGTGGAGTGAATCAACATTTCTAGATCTGATCTACCCTGA
AGAAGAGGCGGAGCGGATCCTCTTTTTTCAAATTTGATCTTCCCTGAAGAAACAGTGGAACAAGT
ATGC
Found at i:674645 original size:13 final size:13
Alignment explanation
Indices: 674627--674653 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
674617 GGAGAAGATC
674627 CATTTTCAAAATT
1 CATTTTCAAAATT
674640 CATTTTCAAAATT
1 CATTTTCAAAATT
674653 C
1 C
674654 TCTCTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (13 bp):
CATTTTCAAAATT
Found at i:674828 original size:3 final size:3
Alignment explanation
Indices: 674822--674867 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
674812 ATCTGACACC
674822 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
674867 A
1 A
674868 ATTTCTTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:676055 original size:107 final size:106
Alignment explanation
Indices: 675919--676120 Score: 273
Period size: 107 Copynumber: 1.9 Consensus size: 106
675909 GTTAGCCACA
* *
675919 TTTTTGCATGTTAGTCACATGTAAGGACCAAAGTTGTCATTTACCTATTTTTACGCATGTTATAT
1 TTTTTGCATGTTAGT-ACATGTAAGGACCAAAGTTGTCATTTACCCATTTTCACGCATGTTATAT
*
675984 ATATTTTG-GAGTATTTGTTATTTAGTCCCCCATAGTTTAGTG
65 ATATTTTGTGA-TATTTATTATTTAGTCCCCCATAGTTTAGTG
* * * *
676026 TTTTTGCATGTTGGT-CATGTATAGGGACCAAAGTTGTTATTTACCCATTTTCATGCATGTTATG
1 TTTTTGCATGTTAGTACATGTA-A-GGACCAAAGTTGTCATTTACCCATTTTCACGCATGTTATA
* *
676090 TATTTTTTGTGATATTTATTGTTTAGTCCCC
64 TATATTTTGTGATATTTATTATTTAGTCCCC
676121 TTTATTTAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 6 0.07
106 1 0.01
107 74 0.89
108 2 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (106 bp):
TTTTTGCATGTTAGTACATGTAAGGACCAAAGTTGTCATTTACCCATTTTCACGCATGTTATATA
TATTTTGTGATATTTATTATTTAGTCCCCCATAGTTTAGTG
Found at i:701758 original size:3 final size:3
Alignment explanation
Indices: 701750--701849 Score: 92
Period size: 3 Copynumber: 31.0 Consensus size: 3
701740 TCTCTCTATA
*
701750 AAT AAT AAT AAT AATT AATT AAT AAT AAT AACT AAT AAT ATT AATT AAT
1 AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AA-T AAT AAT AAT AA-T AAT
* * * *
701799 AAT AAT AAA AATT AAT AAT AAAT GAT AAT AAT AAGT AAT AAC AAA AAT
1 AAT AAT AAT AA-T AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AAT AAT
701847 AAT
1 AAT
701850 TCGAACAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
3 61 0.74
4 21 0.26
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:701768 original size:13 final size:12
Alignment explanation
Indices: 701750--701849 Score: 92
Period size: 13 Copynumber: 7.8 Consensus size: 12
701740 TCTCTCTATA
701750 AATAATAATAAT
1 AATAATAATAAT
701762 AATTAATTAATAAT
1 AA-TAA-TAATAAT
701776 AATAACTAATAAT
1 AATAA-TAATAAT
*
701789 ATTAATTAATAAT
1 AATAA-TAATAAT
*
701802 AATAAAAATTAAT
1 AATAATAA-TAAT
*
701815 AATAAATGATAAT
1 AAT-AATAATAAT
*
701828 AATAAGTAATAAC
1 AATAA-TAATAAT
*
701841 AAAAATAAT
1 AATAATAAT
701850 TCGAACAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.14
13 51 0.70
14 12 0.16
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:701792 original size:26 final size:25
Alignment explanation
Indices: 701750--701839 Score: 108
Period size: 26 Copynumber: 3.4 Consensus size: 25
701740 TCTCTCTATA
701750 AATAATAATAATAATTAATTAATAAT
1 AATAATAATAAT-ATTAATTAATAAT
701776 AATAACTAATAATATTAATTAATAAT
1 AATAA-TAATAATATTAATTAATAAT
* * * *
701802 AATAAAAATTAATAATAAATGATAAT
1 AATAATAA-TAATATTAATTAATAAT
701828 AATAAGTAATAA
1 AATAA-TAATAA
701840 CAAAAATAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
25 2 0.04
26 45 0.80
27 9 0.16
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (25 bp):
AATAATAATAATATTAATTAATAAT
Found at i:710074 original size:14 final size:14
Alignment explanation
Indices: 710055--710085 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
710045 GATCTGACAA
710055 TGTAATGAGTATGT
1 TGTAATGAGTATGT
710069 TGTAATGAGTATGT
1 TGTAATGAGTATGT
710083 TGT
1 TGT
710086 CCTTGCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
TGTAATGAGTATGT
Found at i:715005 original size:2 final size:2
Alignment explanation
Indices: 714998--715052 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
714988 TTATTGGGTG
714998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
715040 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
715053 GCTTAAGGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:716286 original size:24 final size:24
Alignment explanation
Indices: 716258--716311 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
716248 TACGGGACAT
* *
716258 TTCTACATGGTCCTTCAGGACAAA
1 TTCTACACGGTCCTTCAGGAAAAA
* **
716282 TTCTACGCGGTCCTTTGGGAAAAA
1 TTCTACACGGTCCTTCAGGAAAAA
716306 TTCTAC
1 TTCTAC
716312 GTGGCACTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (24 bp):
TTCTACACGGTCCTTCAGGAAAAA
Found at i:718005 original size:3 final size:3
Alignment explanation
Indices: 717997--718105 Score: 74
Period size: 3 Copynumber: 33.7 Consensus size: 3
717987 TCTATAAATA
* * * *
717997 AAT AAT AATT AATT AAT AAC AATT AAT AAC AAT AAT AAT AATT ATT ATT
1 AAT AAT AA-T AA-T AAT AAT AA-T AAT AAT AAT AAT AAT AA-T AAT AAT
* * * *
718046 AAT AACT AAT GAT AGT AATT AAT AAT AAT AAT AAT AAT AAAT GAT AAA
1 AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT
718094 AAT AAGT AAT AA
1 AAT AA-T AAT AA
718106 CAAAAATAAC
Statistics
Matches: 85, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
3 62 0.73
4 23 0.27
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:718022 original size:10 final size:10
Alignment explanation
Indices: 718007--718040 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
717997 AATAATAATT
718007 AATTAATAAC
1 AATTAATAAC
718017 AATTAATAAC
1 AATTAATAAC
*
718027 AA-TAATAAT
1 AATTAATAAC
718036 AATTA
1 AATTA
718041 TTATTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTAATAAC
Found at i:718070 original size:39 final size:33
Alignment explanation
Indices: 717997--718085 Score: 92
Period size: 35 Copynumber: 2.6 Consensus size: 33
717987 TCTATAAATA
717997 AATAATAATTAATTAATAACAATTAATAACAAT
1 AATAATAATTAATTAATAACAATTAATAACAAT
* *
718030 AATAATAATTATTATTAATAACTAATGATAGTAATTAAT
1 AATAATAATTA--ATTAATAAC-AAT--TAATAA-CAAT
718069 AATAATAA-TAA-TAATAA
1 AATAATAATTAATTAATAA
718086 ATGATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
33 11 0.23
35 15 0.31
36 4 0.08
38 7 0.15
39 11 0.23
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.36
Consensus pattern (33 bp):
AATAATAATTAATTAATAACAATTAATAACAAT
Found at i:723888 original size:20 final size:20
Alignment explanation
Indices: 723834--723888 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
723824 CCTATTTAAG
*
723834 TGGTATCGATACCAAGAGGA
1 TGGTATCGATACCATGAGGA
** *
723854 AAGTATAGATACCATGAGGA
1 TGGTATCGATACCATGAGGA
723874 TGGTATCGATACCAT
1 TGGTATCGATACCAT
723889 TGATCACAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (20 bp):
TGGTATCGATACCATGAGGA
Found at i:724567 original size:81 final size:81
Alignment explanation
Indices: 724380--725169 Score: 940
Period size: 81 Copynumber: 9.7 Consensus size: 81
724370 GTGTCTTTGA
* * * * * *
724380 GGCCTAGTTGTGCATTTAGAAGAAATGTGTCAATGATGTCAGTAAGATGAACGGTTAAAGAACGT
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
724445 T-AGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
** * * * * **
724460 GGCCTAGCTACGCATCTAGAAGAAAGGTGTCAATAATGCCAGTTAGATGAATGGTTAAAGACTAT
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
724525 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * *
724541 GGCCTAGCTGTGAATTTGGCATAAAGGTGTCAATGATGCCAGTTAGATGAACAGTTAAAGACTGT
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
724606 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
724622 GGCATAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
* *
724687 TAAGTAAAAGATATAT
66 TGAGTAAAAGATAAAT
* * * * * *
724703 GGCCTGGTTGTGTATTTTGAAGAAAGGTATCAATGATGCCAGTTAGATGAAAGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
*
724768 TGAACAGTTAAAGATAAAT
66 TG---AGTAAAAGATAAAT
* * * * * *
724787 GGCCCAGCTGTGCATTTGGAAGAAAGGTTTCAAT-ATTTCCAGTTAGATGAACGATTAAAGATCA
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGA-TGCCAGTTAGATGAACGGTTAAAGACCG
724851 TTGAGTAAAAGATAAAT
65 TTGAGTAAAAGATAAAT
* * * * * * *
724868 GCCCTAGCTGTGCATTTGGAACAGAGTTGTCAATGATGCTAGTTAGATGAATGGTTAAAGACCAT
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
724933 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
724949 GGCCTAGTTGTGCATTTGGTAGAAAGTTGTCAATTATGCTAGTTAGATGAACAGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
*
725014 TGAGAAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
725030 GGCCTAGCTATGCATTTGGCATAATA-GTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCG
1 GGCCTAGCTGTGCATTTGGAAGAA-AGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCG
* *
725094 TTGAATAAAAAATAAAT
65 TTGAGTAAAAGATAAAT
* * * * *
725111 GGCCTAGCTGTGCATTTAGAAGACAA-GTGTCAATCATGCAAATTAGATGAAAGGTTAAA
1 GGCCTAGCTGTGCATTTGGAAGA-AAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAA
725170 TGCGTTTGGG
Statistics
Matches: 608, Mismatches: 94, Indels: 15
0.85 0.13 0.02
Matches are distributed among these distances:
80 54 0.09
81 484 0.80
82 3 0.00
83 1 0.00
84 66 0.11
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:725071 original size:327 final size:325
Alignment explanation
Indices: 724380--725161 Score: 1009
Period size: 327 Copynumber: 2.4 Consensus size: 325
724370 GTGTCTTTGA
* * * * * * *
724380 GGCCTAGTTGTGCATTTAGAAGAAATGTGTCAATGATGTCAGTAAGATGAACGGTTAAAGAACGT
1 GGCCTAGCTATGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
** *
724445 T--AGTAAAAGATAAATGGCCTAGCTACGCATCTAGAAGAAAGGTGTCAATAATGCCAGTTAGAT
66 TGAAGTAAAAGATAAATGGCCTAGCTGTGCATTTAGAAGAAAGGTGTCAATAATGCCAGTTAGAT
* * * * *
724508 GAATGGTTAAAGACTATTGAGTAAAAGATAAATGGCCTAGCTGTGAATTTGGCATAAAGGTGTCA
131 GAACGATTAAAGACTATTGAGTAAAAGATAAATGCCCTAGCTGTGAATTTGGAACAAAGGTGTCA
**
724573 ATGATGCCAGTTAGATGAACAGTTAAAGACTGTTGAGTAAAAGATAAATGGCATAGCTGTGCATT
196 ATGATGCCAGTTAGATGAACAGTTAAAGACCATTGAGTAAAAGATAAATGGCATAGCTGTGCATT
* * *
724638 TGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATATAT
261 TGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGACCGTTAAGAAAAAGATAAAT
* * * * * * *
724703 GGCCTGGTTGTGTATTTTGAAGAAAGGTATCAATGATGCCAGTTAGATGAAAGGTTAAAGACCGT
1 GGCCTAGCTATGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
* * * * * *
724768 TGAACAGTTAAAGATAAATGGCCCAGCTGTGCATTTGGAAGAAAGGTTTCAATATTTCCAGTTAG
66 TG-A-AGTAAAAGATAAATGGCCTAGCTGTGCATTTAGAAGAAAGGTGTCAATAATGCCAGTTAG
* * *
724833 ATGAACGATTAAAGA-TCATTGAGTAAAAGATAAATGCCCTAGCTGTGCATTTGGAACAGAGTTG
129 ATGAACGATTAAAGACT-ATTGAGTAAAAGATAAATGCCCTAGCTGTGAATTTGGAACAAAGGTG
* ** * *
724897 TCAATGATGCTAGTTAGATGAATGGTTAAAGACCATTGAGTAAAAGATAAATGGCCTAGTTGTGC
193 TCAATGATGCCAGTTAGATGAACAGTTAAAGACCATTGAGTAAAAGATAAATGGCATAGCTGTGC
* * * *
724962 ATTTGGTAGAAAGTTGTCAATTATGCTAGTTAGATGAACAGTTAAAGACCGTTGAGAAAAAGATA
258 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGACCGTTAAGAAAAAGATA
725027 AAT
323 AAT
* * *
725030 GGCCTAGCTATGCATTTGGCATAATA-GTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCG
1 GGCCTAGCTATGCATTTGGAAGAA-AGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCG
* * * *
725094 TTGAA-TAAAAAATAAATGGCCTAGCTGTGCATTTAGAAGACAA-GTGTCAATCATGCAAATTAG
65 TTGAAGTAAAAGATAAATGGCCTAGCTGTGCATTTAGAAGA-AAGGTGTCAATAATGCCAGTTAG
725157 ATGAA
129 ATGAA
725162 AGGTTAAATG
Statistics
Matches: 392, Mismatches: 60, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
323 57 0.15
324 50 0.13
325 3 0.01
326 2 0.01
327 279 0.71
328 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (325 bp):
GGCCTAGCTATGCATTTGGAAGAAAGGTGTCAATGATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAAGTAAAAGATAAATGGCCTAGCTGTGCATTTAGAAGAAAGGTGTCAATAATGCCAGTTAGAT
GAACGATTAAAGACTATTGAGTAAAAGATAAATGCCCTAGCTGTGAATTTGGAACAAAGGTGTCA
ATGATGCCAGTTAGATGAACAGTTAAAGACCATTGAGTAAAAGATAAATGGCATAGCTGTGCATT
TGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGACCGTTAAGAAAAAGATAAAT
Found at i:728824 original size:21 final size:19
Alignment explanation
Indices: 728781--728818 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
728771 TTATGTAAGC
728781 TTAAGGAAAGATTATATGA
1 TTAAGGAAAGATTATATGA
728800 TTAAGGAAAGATTATATGA
1 TTAAGGAAAGATTATATGA
728819 GATTAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (19 bp):
TTAAGGAAAGATTATATGA
Found at i:729327 original size:22 final size:21
Alignment explanation
Indices: 729296--729336 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
729286 TCGGTATCGT
729296 AATAGAGTATCGATACCATAG
1 AATAGAGTATCGATACCATAG
729317 AATAGTAGTATCGATACCAT
1 AATAG-AGTATCGATACCAT
729337 GATGGGGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (21 bp):
AATAGAGTATCGATACCATAG
Found at i:729757 original size:55 final size:54
Alignment explanation
Indices: 729691--729844 Score: 193
Period size: 55 Copynumber: 2.8 Consensus size: 54
729681 TTAAGCGTGA
* *
729691 AAAACTTAAGAAATCCATACTAAGTGTATGAATTTCAGTATGGGCACTTTGTGTGC
1 AAAAC-TAAGAAATTCATACTAAGTGTATGAATTTC-GTATGGGCACTATGTGTGC
* * *
729747 AAAACTAAGAAATTCATACTAAGTGTACGAATTTCCGTATGAGCACTATGTGTTC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTT-CGTATGGGCACTATGTGTGC
* *
729802 -AAACTAAGAAAATTCATACTAGGTGTATAAATTTTCGTATGGG
1 AAAACTAAG-AAATTCATACTAAGTGTATGAA-TTTCGTATGGG
729845 AAATAAATGT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
54 8 0.09
55 69 0.80
56 9 0.10
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (54 bp):
AAAACTAAGAAATTCATACTAAGTGTATGAATTTCGTATGGGCACTATGTGTGC
Found at i:730129 original size:16 final size:16
Alignment explanation
Indices: 730108--730142 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
730098 TTATATGAAA
*
730108 GGCTAAGTGCCTTTGC
1 GGCTAACTGCCTTTGC
730124 GGCTAACTGCCTTTGC
1 GGCTAACTGCCTTTGC
730140 GGC
1 GGC
730143 CTAGCTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.31, T:0.29
Consensus pattern (16 bp):
GGCTAACTGCCTTTGC
Found at i:730247 original size:81 final size:81
Alignment explanation
Indices: 730140--731006 Score: 1074
Period size: 81 Copynumber: 10.7 Consensus size: 81
730130 CTGCCTTTGC
* * * * *
730140 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATGATGCTAGTTAGATGAACGGTTAAAGATCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
* *
730205 TAACTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * ** * *
730221 GGCCTAGTTTTGCATTTGGCATAAAGGTACCAATTATACCAGTTAGATGAAAGGTTAAAGACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
730286 TGAATAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* ** * *
730302 GGCCTAGTTGTGCATTTGGCATAAAGGTACCAATTATACCAGTTAGATGAAAGGTTAAAGACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
730367 TGAATAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
730383 GGCCTAGTTGTGCA-TTGGCATAAAGGTGTCAATGATGCCAGTTAGATGAACAGTTAAAGATCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
730447 TGAGTAAAAAATAAAT
66 TGAGTAAAAGATAAAT
* * *** * * *
730463 GGCCTAGTTGTGCATTTAGCATAAAGGCACCAATTATACCAATTAGATGAAAGGTTAAAGACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
730528 TGAATAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
730544 GGCCTAGTTGAGCA-TTGGCAGAAAGGTGTCAATGATGCCAGTTAGATGAACGATTAAAGACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
730608 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
730624 TGCCTAGCTGTGTATTTGGTAGAAAGGTGTCAATTATACTAGTTAGATGAACGGTTAAAGACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
730689 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * *
730705 GGCCTAGTTGTGCATTTGGTAGAAAGGTGTCAATGATACCAGTTAGATGAATGGTTAAAGACCAT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
730770 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * ** * *
730786 GGCCTAGTTATGCATTGGGAAGAAAGGTGTCAATTATGATAGTTAGATGAACGATTAAAGACTGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
730851 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * * *
730867 GGTCTAGTTGTGCATTTGGAAGAGATGTGTCAATTATGCCAATTAAATGAATGGTTAAAGACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
730932 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * ** * *
730948 GGCCTAGCTATGCATTTAGCAGACAA-ATGTCAATCGTGCAAGTTAGATGAAAGGTTAAA
1 GGCCTAGTTGTGCATTTGGCAGA-AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAA
731007 TGCATTTGGG
Statistics
Matches: 684, Mismatches: 99, Indels: 6
0.87 0.13 0.01
Matches are distributed among these distances:
80 136 0.20
81 547 0.80
82 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:733840 original size:16 final size:16
Alignment explanation
Indices: 733819--733851 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
733809 ACATCAAACA
*
733819 TGTATTGTTCCTTTTT
1 TGTATTGCTCCTTTTT
733835 TGTATTGCTCCTTTTT
1 TGTATTGCTCCTTTTT
733851 T
1 T
733852 ACCGTTCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.12, T:0.67
Consensus pattern (16 bp):
TGTATTGCTCCTTTTT
Found at i:749096 original size:12 final size:12
Alignment explanation
Indices: 749079--749109 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
749069 CCGGGTATTG
*
749079 ATCCCCGTCCCC
1 ATCCCCGTACCC
749091 ATCCCCGTACCC
1 ATCCCCGTACCC
749103 ATCCCCG
1 ATCCCCG
749110 CTTAAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.61, G:0.10, T:0.16
Consensus pattern (12 bp):
ATCCCCGTACCC
Found at i:754287 original size:23 final size:24
Alignment explanation
Indices: 754261--754315 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
754251 TTTACTTTTA
754261 TTTTAATTATTAA-AATTTAAAT-T
1 TTTTAATT-TTAATAATTTAAATCT
*
754284 TTTTAA-TTTAATCATTTAAATCT
1 TTTTAATTTTAATAATTTAAATCT
754307 TTTTAATTT
1 TTTTAATTT
754316 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 9 0.32
23 13 0.46
24 2 0.07
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTAATTTTAATAATTTAAATCT
Found at i:766203 original size:60 final size:60
Alignment explanation
Indices: 766124--766808 Score: 1012
Period size: 60 Copynumber: 11.4 Consensus size: 60
766114 TTATGCCGTT
* * *
766124 AATGCACCGTTAGGCATTTACCTTTTCATCTAACTTGCATTAGTGACACCTTTCTACCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * * *
766184 AATACACAGTTAGGCATTTAACTTTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * *
766244 AATGTACCATTAGGCATTTAACTTTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * * * *
766304 AGTGCACCTTTAGGCATTTAACTTTTCATCTAACATGCATTAGTGGTACCTTTATGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * * *
766364 AATGC-CCTTTTAGACATTTAACTTTTCATCTAACTTGCATTAGTTGTACCTTTCTGCCAA
1 AATGCACC-GTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * * * *
766424 AATGCACCGTTATGCATTTATCTTTTCATCTAACTTGCATTAATGACACCTTTCTACCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* *
766484 AATGCACCGTTAGGCATTTAACTTTTCGTCTAACTTGGATTAGTGGCACCTTTCTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* *
766544 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTATTGGCACCTTTCTGCTAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * *
766604 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGTACCTTTCTACAAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* *
766664 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * * *
766724 AATGCACCGCTAGGCATTTAAGTTTTCATCTAACTTGCATTATTGGCACCTTTTTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
*
766784 AATGCACCGTTAGACATTTAACTTT
1 AATGCACCGTTAGGCATTTAACTTT
766809 CATTTTAGAG
Statistics
Matches: 564, Mismatches: 59, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
59 2 0.00
60 560 0.99
61 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (60 bp):
AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
Found at i:768749 original size:13 final size:13
Alignment explanation
Indices: 768731--768756 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
768721 GACTGGGAGC
768731 TTATGTGAAAATG
1 TTATGTGAAAATG
768744 TTATGTGAAAATG
1 TTATGTGAAAATG
768757 GGATAAAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TTATGTGAAAATG
Found at i:781571 original size:85 final size:85
Alignment explanation
Indices: 781465--781682 Score: 305
Period size: 85 Copynumber: 2.6 Consensus size: 85
781455 GCAATTGTGT
* * * *
781465 GTCATAAATCTATAACGCGCAT-TAATGACGTT-CTTTGAGTGTCATTGAAGCTCCCATCATAAA
1 GTCATAAATCTATGACACGCATGT-ATGAC-TTACATTGAGTGTCATTGAAGCCCCCATCATAAA
781528 TTAAGATGACACACATTTATGC
64 TTAAGATGACACACATTTATGC
* * * *
781550 GTCATAAATGTATGACACGCATGTATGACTTACATTGTGCGTCATTGAAGCCCCCGTCATAAATT
1 GTCATAAATCTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCATCATAAATT
*
781615 AAGATGACACACATTTGTGC
66 AAGATGACACACATTTATGC
* *
781635 GTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGA
1 GTCATAAATCTATGACACGCATGTATGACTTACATTGAGTGTCATTGA
781683 TGCACACGTC
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
84 2 0.02
85 116 0.97
86 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (85 bp):
GTCATAAATCTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCATCATAAATT
AAGATGACACACATTTATGC
Found at i:783107 original size:12 final size:12
Alignment explanation
Indices: 783090--783120 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
783080 ATATATTGAT
783090 AATCAAATGAAA
1 AATCAAATGAAA
783102 AATCAAATGAAA
1 AATCAAATGAAA
*
783114 AAACAAA
1 AATCAAA
783121 CCCGAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:787668 original size:15 final size:15
Alignment explanation
Indices: 787597--787667 Score: 115
Period size: 15 Copynumber: 4.7 Consensus size: 15
787587 GATACTTTCT
787597 TTTTCCTTCTTTGACG
1 TTTT-CTTCTTTGACG
787613 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
787628 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
787643 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
787658 TTGTCTTCTT
1 TTTTCTTCTT
787668 ACCCCATGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
15 49 0.92
16 4 0.08
ACGTcount: A:0.07, C:0.21, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:792062 original size:21 final size:21
Alignment explanation
Indices: 792037--792080 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
792027 AGTCAAGCAA
792037 ATCCCATCATGGAACCCAAAT
1 ATCCCATCATGGAACCCAAAT
792058 ATCCCATCATGGAACCCAAAT
1 ATCCCATCATGGAACCCAAAT
792079 AT
1 AT
792081 ACGATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.20
Consensus pattern (21 bp):
ATCCCATCATGGAACCCAAAT
Found at i:794051 original size:23 final size:24
Alignment explanation
Indices: 793999--794051 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
793989 GATATGTTTA
* * *
793999 TAAATTTTTTTATAATATAAATTT
1 TAAATTCTTTTAAAAGATAAATTT
*
794023 TGAATTCTTTTAAAAGA-AAATTT
1 TAAATTCTTTTAAAAGATAAATTT
794046 TAAATT
1 TAAATT
794052 AAAATTTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
TAAATTCTTTTAAAAGATAAATTT
Done.